Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Ac3H11_2115 Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9)
Query= reanno::pseudo3_N2E3:AO353_15995 (844 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2115 Length = 585 Score = 253 bits (646), Expect = 2e-71 Identities = 184/578 (31%), Positives = 273/578 (47%), Gaps = 40/578 (6%) Query: 277 LRGVCASAGSAFGYVVQVAERTLEMPEFAADQQLERESLERALMH---ATQALQRLRDNA 333 + G+ + G A G V VA +++ + + +ER + LQRL+ + Sbjct: 5 VHGLAVARGIAIGRAVLVASSRVDVAHYFVEPSQVEGEIERVRQGRNAVVEELQRLQTDM 64 Query: 334 AGEAQADI---FKAHQELLEDPSLLEQAQALIAEGK-SAAFAWNSATEATATLFKSLGST 389 +A ++ H LL+D +L + I E +A +A + E A F + Sbjct: 65 PTDAPHELTALLDVHLMLLQDEALTGGVKHWITERLYNAEWALTTQLEVIARQFDEMEDE 124 Query: 390 LLAERALDLMDVGQRVLKLILGVP--------------------DGVWELPDQAILIAEQ 429 L ER DL V +R+L+ + GV D ++P +L+A Sbjct: 125 YLRERKADLEQVVERILRHMKGVASPVAPPASSPRRKTQQDLLLDDTVDVP--LVLVAHD 182 Query: 430 LTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDA 489 L+P+ GF T GG TSH AI+AR++ +PAV G + V++D Sbjct: 183 LSPADMLQFKQSVFAGFVTDVGGKTSHTAIVARSMDIPAVVGARAASQLVRQDDWVIIDG 242 Query: 490 DKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETE 549 D G + +DP+ ++ + +++Q + A+T DGH E+ AN+ + Sbjct: 243 DAGVVIVDPSPIILAEYGFRQRQVELERERLARLRHTPAITIDGHKIELLANIEQPGDAA 302 Query: 550 QAMSLGAEGIGLLRSEFLYQQRSV-APSHDEQAGTYSAIARALGPQRNL--VVRTLDVGG 606 A+ GA G+GL RSEFL+ +S P DEQ Y A A+ + L +RT+DVG Sbjct: 303 AAVRAGAVGVGLFRSEFLFMGKSGNLPGEDEQ---YRAYCEAIDGMQGLPVTIRTIDVGA 359 Query: 607 DKPLAY-VPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAGLARLHIMLPMVSQLS 665 DKPL D+ NP LG+R IR L P + R Q RA+L +A +++++ PM++ Sbjct: 360 DKPLDNKAHKDNYLNPALGLRAIRWSLADPAMFRTQLRAVLRAAAHGKVNLLFPMLAHTH 419 Query: 666 ELRLARLMLEEEALALGLRELP----KLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQ 721 E++ ++ L R P +LG MIEVPAAALM F DF SIGTNDL Q Sbjct: 420 EIQQTLAQVDLARAELDARGEPYGPVQLGAMIEVPAAALMVRTFLKYFDFLSIGTNDLIQ 479 Query: 722 YTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGL 781 YTLA+DR +A D HP+VLRL+ + GK V VCG A + LLLGL Sbjct: 480 YTLAIDRADEAVAHLYDPLHPAVLRLVGDVIAEGERQGKSVCVCGETAGDVTMTRLLLGL 539 Query: 782 GVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLE 819 G+ S+ I AIK + + A QV+G E Sbjct: 540 GLRSFSMHPAQILAIKQEVLRADTRKLAPWAQQVIGGE 577 Lambda K H 0.318 0.132 0.370 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 994 Number of extensions: 42 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 844 Length of database: 585 Length adjustment: 39 Effective length of query: 805 Effective length of database: 546 Effective search space: 439530 Effective search space used: 439530 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory